Coexpression cluster:C3995

Full id: C3995_occipital_cerebral_spinal_small_temporal_heart_rectum

Phase1 CAGE Peaks

Hg19::chr1:72748492..72748510,-	p5@NEGR1
Hg19::chr1:72748523..72748538,-	p3@NEGR1
Hg19::chr1:72748551..72748570,-	p4@NEGR1

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	1.08e-09	180
smooth muscle cell	7.54e-09	42
smooth muscle myoblast	7.54e-09	42
vascular associated smooth muscle cell	4.26e-08	32
muscle precursor cell	4.84e-08	57
myoblast	4.84e-08	57
multi-potent skeletal muscle stem cell	4.84e-08	57
muscle cell	4.25e-07	54

Uber Anatomy

Ontology term	p-value	n
neural tube	2.89e-25	57
neural rod	2.89e-25	57
future spinal cord	2.89e-25	57
neural keel	2.89e-25	57
adult organism	2.48e-24	115
regional part of brain	4.53e-23	59
anterior neural tube	2.99e-21	42
regional part of forebrain	3.80e-21	41
forebrain	3.80e-21	41
future forebrain	3.80e-21	41
brain	2.81e-20	69
future brain	2.81e-20	69
central nervous system	1.07e-19	82
neurectoderm	3.02e-19	90
neural plate	3.57e-19	86
presumptive neural plate	3.57e-19	86
gray matter	2.88e-18	34
brain grey matter	2.88e-18	34
cerebral hemisphere	1.36e-17	32
telencephalon	1.47e-17	34
regional part of nervous system	1.72e-17	94
nervous system	1.72e-17	94
regional part of telencephalon	4.41e-17	33
pre-chordal neural plate	4.05e-16	61
organism subdivision	9.64e-16	365
tube	2.09e-15	194
regional part of cerebral cortex	6.09e-15	22
epithelium	1.91e-14	309
anatomical cluster	2.07e-14	286
cerebral cortex	5.79e-14	25
pallium	5.79e-14	25
cell layer	5.96e-14	312
neocortex	1.15e-13	20
multi-cellular organism	5.55e-13	659
anterior region of body	4.66e-12	129
craniocervical region	4.66e-12	129
head	5.08e-12	123
anatomical conduit	5.83e-12	241
multi-tissue structure	1.02e-11	347
ectoderm	2.04e-10	173
presumptive ectoderm	2.04e-10	173
ectoderm-derived structure	3.72e-10	169
anatomical system	5.06e-10	625
somite	5.12e-10	83
paraxial mesoderm	5.12e-10	83
presomitic mesoderm	5.12e-10	83
presumptive segmental plate	5.12e-10	83
trunk paraxial mesoderm	5.12e-10	83
presumptive paraxial mesoderm	5.12e-10	83
embryonic structure	7.18e-10	605
developing anatomical structure	7.18e-10	605
anatomical group	8.27e-10	626
embryo	8.84e-10	612
germ layer	1.31e-09	604
embryonic tissue	1.31e-09	604
presumptive structure	1.31e-09	604
epiblast (generic)	1.31e-09	604
dermomyotome	2.20e-09	70
muscle tissue	8.71e-09	63
musculature	8.71e-09	63
musculature of body	8.71e-09	63
tissue	9.51e-09	787
skeletal muscle tissue	1.67e-08	61
striated muscle tissue	1.67e-08	61
myotome	1.67e-08	61
blood vessel	1.15e-07	60
epithelial tube open at both ends	1.15e-07	60
blood vasculature	1.15e-07	60
vascular cord	1.15e-07	60
artery	1.66e-07	42
arterial blood vessel	1.66e-07	42
arterial system	1.66e-07	42
systemic artery	6.04e-07	33
systemic arterial system	6.04e-07	33

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115314385831813
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279755414576175
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325748091820081
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000676804937045824
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00664638877774628

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.